A non resident customer who has J1 visa opens an account. He will be working at a hospital next 2 years eligable as an exchange visitor status. (he is a doctor)
Do we fill out W-8 or W-9 for him?

If the person signing the IRS form is a US Person or a US Resident Alien use the W-9. If they are not use the W-8. Here is a link to the IRS' Form W-9 and Form W-8 . The instructions provide additional info that may be useful.